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DNA/Protein structure-function
analysis and prediction
Lecture 11: DNA/RNA structure
Central Dogma of
Molecular Biology
Replication
DNA
Transcription
mRNA
Translation
Protein
Transcription is carried out by RNA polymerase (II)
Translation is performed on ribosomes
Replication is carried out by DNA polymerase
Reverse transcriptase copies RNA into DNA
Transcription + Translation = Expression
But DNA can also be transcribed into
non-coding RNA …
tRNA (transfer): transfer of amino acids to the
ribosome during protein synthesis.
rRNA (ribosomal): essential component of the ribosomes
(complex with rProteins).
snRNA (small nuclear): mainly involved in RNA-splicing
(removal of introns). snRNPs.
snoRNA (small nucleolar): involved in chemical modifications of
ribosomal RNAs and other RNA genes. snoRNPs.
SRP RNA (signal recognition particle): form RNA-protein
complex involved in mRNA secretion.
Further: microRNA, eRNA, gRNA, tmRNA etc.
RNA editing
Eukaryotes have spliced genes …





Promoter: involved in transcription initiation (TF/RNApol-binding sites)
TSS: transcription start site
UTRs: un-translated regions (important for translational control)
Exons will be spliced together by removal of the Introns
Poly-adenylation site important for transcription termination
(but also: mRNA stability, export mRNA from nucleus etc.)
DNA makes mRNA makes Protein
DNA makes mRNA makes Protein
mRNA
Some facts about human genes
 There are about 20.000 – 25.000 genes in the human
genome (~ 3% of the genome)
 Average gene length is ~ 8.000 bp
 Average of 5-6 exons per gene
 Average exon length is ~ 200 bp
 Average intron length is ~ 2000 bp
 8% of the genes have a single exon
 Some exons can be as small as 1 or 3 bp
DMD: the largest known human gene
 The largest known human gene is DMD,
the gene that encodes dystrophin:
~ 2.4 milion bp over 79 exons
 X-linked recessive disease (affects boys)
 Two variants: Duchenne-type (DMD) and
Becker-type (BMD)
 Duchenne-type: more severe,
frameshift-mutations
Becker-type: milder phenotype, “in
frame”- mutations
Posture changes during progression
of Duchenne muscular dystrophy
Nucleic acid basics
 Nucleic acids are polymers
nucleotide
nucleoside
 Each monomer consists of 3
moietics
Nucleic acid basics (2)
 A base can be of 5 rings
 Purines and Pyrimidines
can base-pair (WatsonCrick pairs)
Watson and Crick, 1953
Nucleic acid as hetero-polymers
 Nucleosides, nucleotides
(Ribose sugar,
RNA precursor)
 DNA and RNA strands
(2’-deoxy ribose sugar,
DNA precursor)
REMEMBER:


(2’-deoxy thymidine triphosphate, nucleotide)

DNA = deoxyribonucleotides;
RNA = ribonucleotides (OH-groups at
the 2’ position)
Note the directionality of DNA (5’-3’
& 3’-5’) or RNA (5’-3’)
DNA = A, G, C, T ; RNA = A, G, C, U
So …
DNA
RNA
Stability of base-pairing
 C-G base pairing is more stable than A-T (A-U) base
pairing (why?)
 3rd codon position has freedom to evolve (synonymous
mutations)
 Species can therefore optimise their G-C content (e.g.
thermophiles are GC rich) (consequences for codon use?)
Thermocrinis ruber, heat-loving bacteria
DNA compositional biases
 Base compositions of genomes: G+C (and therefore also
A+T) content varies between different genomes
 The GC-content is sometimes used to classify organism in
taxonomy
 High G+C content bacteria: Actinobacteria
e.g. in Streptomyces coelicolor it is 72%
Low G+C content: Plasmodium falciparum (~20%)
 Other examples:
Saccharomyces cerevisiae (yeast)
38%
Arabidopsis thaliana (plant)
36%
Escherichia coli (bacteria)
50%
Genetic diseases: cystic fibrosis
 Known since very early on
(“Celtic gene”)
 Autosomal, recessive,
hereditary disease (Chr. 7)
 Symptoms:
 In exocrine glands (which
produce sweat and mucus)
 Abnormal secretions
 Respiratory problems
 Reduced fertility and (male)
anatomical anomalies
3,000
30,000
20,000
cystic fibrosis (2)
 Gene product: CFTR (cystic fibrosis transmembrane
conductance regulator)
 CFTR is an ABC (ATP-binding cassette) transporter
or traffic ATPase.
 These proteins transport molecules such as sugars,
peptides, inorganic phosphate, chloride, and metal
cations across the cellular membrane.
 CFTR transports chloride ions (Cl-) ions across the
membranes of cells in the lungs, liver, pancreas,
digestive tract, reproductive tract, and skin.
cystic fibrosis (3)
 CF gene CFTR has 3-bp deletion leading to Del508
(Phe) in 1480 aa protein (epithelial Cl- channel)
 Protein degraded in ER instead of inserted into cell
membrane
Diagram depicting the five domains of the
CFTR membrane protein (Sheppard 1999).
Theoretical Model of NBD1. PDB
identifier 1NBD as viewed in Protein
Explorer http://proteinexplorer.org
Let’s return to DNA and RNA
structure …
 Unlike three dimensional structures of proteins,
DNA molecules assume simple double helical
structures independent on their sequences.
 There are three kinds of double helices that have
been observed in DNA: type A, type B, and type Z,
which differ in their geometries.
 RNA on the other hand, can have as diverse
structures as proteins, as well as simple double
helix of type A.
 The ability of being both informational and diverse
in structure suggests that RNA was the prebiotic
molecule that could function in both replication and
catalysis (The RNA World Hypothesis).
 In fact, some viruses encode their genetic materials
by RNA (retrovirus)
Three dimensional structures of
double helices
Side view: A-DNA, B-DNA, Z-DNA
Space-filling models of A, B and Z- DNA
Top view: A-DNA, B-DNA, Z-DNA
Major and minor grooves (1)
Major and minor grooves (2)

The major groove is approximately 50%
wider than the minor.

Proteins that interact with DNA often make
contact with the edges of the base pairs
that protrude into the major groove.
Forces that stabilize nucleic acid
double helix
 There are two major forces that contribute to stability of
helix formation:
 Hydrogen bonding in base-pairing
 Hydrophobic interactions in base stacking
5’
3’
3’
5’
Same strand stacking
cross-strand stacking
Types of DNA double helix
 Type A
 Type B
 Type Z
major conformation RNA
minor conformation DNA
major conformation DNA
minor conformation DNA
Right-handed helix
Short and broad
Right-handed helix
Long and thin
Left-handed helix
Longer and thinner
Right handed B-DNA
Secondary structures of Nucleic
acids
 DNA is primarily
in duplex form
 RNA is normally
single stranded
which can have a
diverse form of
secondary
structures other
than duplex.
Non B-DNA Secondary structures
 Cruciform DNA
 Slipped DNA
 Triple helical DNA
Hoogsteen basepairs
Source: Van Dongen et al. (1999) , Nature Structural Biology 6, 854 - 859
More Secondary structures
 RNA pseudoknots
 Cloverleaf rRNA structure
16S rRNA Secondary Structure Based on
Phylogenetic Data
Source: Cornelis W. A. Pleij in Gesteland, R. F. and Atkins, J. F. (1993)
THE RNA WORLD. Cold Spring Harbor Laboratory Press.
3D structures of RNA :
transfer-RNA structures
 Secondary structure
of tRNA (cloverleaf)
 Tertiary structure
of tRNA
3D structures of RNA :
ribosomal-RNA structures
 Secondary structure
of large rRNA (16S)
 Tertiary structure
of large rRNA subunit
Ban et al., Science 289 (905-920), 2000
3D structures of RNA :
Catalytic RNA
 Secondary structure
of self-splicing RNA
 Tertiary structure
of self-splicing RNA
Some structural rules …
 Base-pairing is stabilizing
 Un-paired sections (loops) destabilize
 3D conformation with interactions
makes up for this
Final notes
 Sense/anti-sense RNA
antisense RNA blocks translation through
hybridization with coding strand
Example. Tomatoes synthesize ethylene in order to ripe. Transgenic
tomatoes have been constructed that carry in their genome an
artificial gene (DNA) that is transcribed into an antisense RNA
complementary to the mRNA for an enzyme involved in ethylene
production  tomatoes make only 10% of normal enzyme amount.
 Sense/anti-sense peptides
Have been therapeutically used
Especially in cancer and anti-viral therapy
 Sense/anti-sense proteins
Does it make (anti)sense?
Codons for hydrophilic and hydrophobic amino acids on
the sense strand may sometimes be complemented, in
frame, by codons for hydrophobic and hydrophilic amino
acids on the antisense strand. Furthermore, antisense
proteins may sometimes interact with high specificity
with the corresponding sense proteins… BUT
VERY RARE: HIGHLY CONSERVED CODON BIAS